Kody,
A standard CAD user must know the principles behind styles, templates and libraries in order to use them properly and efficiently. It's 'dangerous' for people to use something they know nothing about.
You may think your not accessing the same files but does Inventor? Regardless of how many precautions you take data may still be lost, overridden or modified without your knowledge when running two instances of Inventor. If you continue to still use this practice all I can say is good luck.
Regards,
Stewart
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Stew, AICP
Inventor Professional 2013, Autodesk Simulation Multiphysics 2013
Windows 7 x64 Core i7 32GB Ram FX2000